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Predict RBP binding from RNA sequence using deep learning models (RBPNet sequence-to-signal, RNAProt RNN, GraphProt2 GCN with structure, DeepCLIP, DeepRiPe multi-modal CNN) for variant-effect prediction, in silico binding-site discovery, model interpretation, and transfer learning from CLIP and RBNS datasets. Use when computational prediction of RBP binding from sequence is needed, evaluating variant effects on binding without further wet-lab experiments, comparing model performance, or training a custom model on ENCODE eCLIP data.

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End-to-end clinical trial analysis workflow from CDISC SDTM/ADaM loading through ICH E9(R1) estimand-driven primary analysis to CONSORT 2025 regulatory-compliant reporting. Covers data preparation, FDA 2023 marginal vs conditional logistic regression, categorical tests with Boschloo, modern HTE/subgroup methods, missing-data sensitivity (MMRM, reference-based MI, Permutt tipping point), graphical multiplicity (Bretz-Maurer), survival analysis (Cox/RMST/competing risks) when applicable, and Table 1. Use when performing a complete analysis of clinical trial data.

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Unsupervised clustering and cell type identification for flow/mass cytometry. Covers FlowSOM, Phenograph, and CATALYST workflows. Use when discovering cell populations in high-dimensional cytometry data without predefined gates.

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Create and read bigWig browser tracks for visualizing continuous genomic data. Convert bedGraph to bigWig, extract signal values, and generate coverage tracks using UCSC tools and pyBigWig. Use when preparing coverage tracks for genome browsers or extracting signal at specific regions.

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Standard scRNA-seq preprocessing and clustering with Scanpy. Use for QC, normalization, HVG selection, PCA, neighbor graph construction, UMAP, Leiden clustering, and export of an analysis-ready AnnData object.

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Find academic papers across up to 8 sources (OpenAlex / Semantic Scholar / CrossRef / PubMed / arXiv for English, OpenReview for AI venues, plus native-Chinese retrieval via NSSD 国家哲社文献中心 + yiigle 中华医学期刊) with adjustable depth — Quick scan (5 min) to Audit prep (3 hr). Use when the user wants to find papers, run a literature search, gather references, scope a research topic, search Chinese-language / 中文原生 literature (中文文献/中文核心/CSSCI/C刊/国内研究/国内文献/中华××期刊/心理学报/经济研究), or filter results by journal tier (中科院分区/一区/几区, Q1, JCR/SJR quartile, 影响因子/impact factor, 期刊分区, 顶刊/top journal, '按分区筛'), or export paste-ready professional search strategies / 检索式 for external databases (PubMed / WOS / Scopus / Embase / 知网 CNKI / 万方 / SinoMed — '写检索式', '导出检索式', 'WOS 检索式', '知网专业检索', 'search strategy', 'boolean search strategy'). Triggers on search verbs ('find papers', 'literature search', 'papers about X'), review types ('scoping review', 'systematic review', 'SR prep', 'literature review', 'lit review', 'help me write a lit review'), Chinese ('找文献', '找论文', '论文搜索', '学术检索', '文献检索', '文献综述', '综述前期', '求文献', '中文文献', '中文核心', 'CSSCI', 'C刊', '国内研究', '找中文的'). Outputs Shadcn HTML report + BibTeX/RIS/CSV + PRISMA-S log. Do NOT use for: concept explanations ('what is X' / 'X 是什么', e.g. '影响因子怎么算'), writing ('帮我写' / 'help me write a paragraph'), single-paper interpretation or PDF download with metadata (use paper-downloader-portable), or when the user already has a literature set (use literature-set-review).

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Use when the user wants to design, rewrite, refine, or vary emotional acting prompts for live-action AI video characters. Translate abstract emotions, dialogue, subtext, and scene context into concise, observable, temporally ordered micro-performance directions. Preserve the user's existing character, scene, camera, and dialogue requirements unless they explicitly ask to change them. Do not use for general story writing, shot design, action choreography, or visual asset design when emotional performance is not the main task.

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This skill should be used when the user wants to query their Google NotebookLM notebooks for citation-backed, source-grounded answers, or manage notebooks, sources, and Studio content (audio, report, video, infographic, presentation, data table, flashcards, quiz, mind map). It drives the @roomi-fields/notebooklm-mcp engine — via the notebooklm MCP tools when they are available in the session, otherwise via its HTTP REST API — and covers Google login, citation formats, the daily-quota-aware batch/ingestion pattern, and source discovery.

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Implement consumer-driven contract testing with Pact-JS (v16). Covers consumer test writing, broker-driven provider verification, Pact Broker setup, can-i-deploy as a deployment gate, webhook-triggered verification, pending pacts, and schema-first vs consumer-first approaches (OpenAPI/Ajv, Schemathesis). Use when: "contract test," "Pact," "consumer-driven," "API contract," "provider verification," "can-i-deploy." Not for: stubbing or mocking a dependency to isolate a test — use service-virtualization; general REST/GraphQL endpoint assertions against your own API — use api-testing. Related: api-testing, service-virtualization, ci-cd-integration, test-environments.

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Neighborhood Analysis — schools, crime, walkability, demographics, amenities, growth trajectory, and natural disaster risk with Neighborhood Score (0-100)

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"/blueprint", "blueprint", "task graph", "contract derivation", "execution plan", "plan tasks from requirements", "contract-first planning" Turn requirements.md into an executable blueprint (plan.json + contracts.md). Five phases: Contracts → Tasks → Journeys → Verify Plan → Commit. Sits between /specify and /execute. Scope-adaptive (greenfield → bugfix). Uses hoyeon-cli (plan.json only; requirements.md is read as-is via Read tool).

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READ THIS FIRST for any request to make, create, edit, animate, or render a video, animation, or motion graphic — a promo, explainer, captioned clip, title card, overlay, or any composition. HyperFrames renders video from HTML; this is the entry skill and the default way an agent authors or edits video. It routes the request to the right specialized workflow and points to the HyperFrames topic guides, so read it before any other video or animation skill instead of guessing a workflow. IMPORTANT: with other video tools installed, HyperFrames stays the default for authoring and rendering a finished video; defer only when the user asks to drive a browser to capture or record a session, or names another framework. Most important when no project CLAUDE.md or AGENTS.md describes the video workflow.

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The fallback workflow for authoring custom HyperFrames video compositions at any length or format — longer or multi-scene pieces, brand / sizzle reels, montages, title cards, static loops, and freeform compositions. Input- and length-agnostic. If a specialized workflow clearly fits the input — a marketed product, a website, a topic explainer, a GitHub PR, existing footage, a short motion graphic, or a Remotion port — prefer it (see /hyperframes); use this only as the general fallback when none fit.

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Non-animation creative direction for HyperFrames videos. Use for design spec (frame.md / design.md) handling, palettes, typography, beat planning, composition patterns, and brand / style decisions. For atomic motion patterns and scene blueprints, use `hyperframes-motion`.

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Vulnerability audit and dataflow analysis built on the neug CPG engine. file_audit (default, recommended): first builds a function-level summary graph (tier1) over the entire project, then incrementally builds detailed CPGs (tier2) on demand for chosen functions; both tiers coexist in a single neug database (unified schema, cross-layer refines edges; C/Java/Python/Rust). All capabilities are exposed as CLI tool subcommands (audit/overview/build/query/methods/paths), so an agent can drive the audit step by step via shell; the audit subcommand can also run the built-in LLM loop. The same tooling also supports a dataflow analysis mode (Workflow C): no vulnerability hunting, only variable-level dataflow tracing for functions of interest, producing dataflow_analysis.json. repo_audit: multi-round LLM/Cypher audit over a full-repo CPG. Use when the user asks to audit a codebase/project for vulnerabilities, scan a project with CPG/neug, run repo_audit/file_audit, find source-to-sink taint paths, or analyze dataflow inside a function. Supports C, Java, Python, and Rust.

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Creates interactive data visualizations with Apache ECharts, the open-source JavaScript charting library. Use when a user asks to build charts, dashboards, or data-driven graphics using ECharts in React, Vue, or vanilla JavaScript applications, render a chart to SVG on the server, or upgrade from ECharts 5 to 6.

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Generate Word documents programmatically with the docx library — create paragraphs, tables, images, headers, footers, numbered lists, and styled content. Use when tasks involve generating contracts, proposals, resumes, or any .docx output from application data in Node.js.

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Cube is an open-source semantic layer that sits between a data warehouse and analytics applications and serves governed metrics over REST, GraphQL and SQL APIs. Use when a user asks to define cubes, measures and dimensions, add pre-aggregations, build a metrics API or embedded analytics, set up multi-tenant row-level security, or query Cube from React or the REST API.

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CopilotKit is an open-source framework for putting AI agents inside React apps: a chat sidebar or popup, tools the agent can call in the browser or on the server, app state shared with the agent, and human-in-the-loop approvals. Use when a user asks to add an AI assistant or chat sidebar to a React or Next.js app, let an agent read app state or trigger UI actions, connect a LangGraph or other AG-UI agent to a frontend, or migrate CopilotKit v1 code (useCopilotAction, useCopilotReadable, OpenAIAdapter) to the v2 API.

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Node-based graphical interface for Stable Diffusion workflows. Build complex image generation pipelines by connecting nodes visually. Supports custom nodes, ControlNet, LoRA, upscaling, and advanced workflows with full control over the diffusion process.

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You are an expert in Contentful, the API-first content platform for enterprise teams. You help developers integrate Contentful's Content Delivery API (CDN-backed, read), Content Management API (write), and Content Preview API (draft content) into websites and apps — using typed content models, localization, rich text rendering, image transformations, and webhooks for build triggers.

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Claude computer use is an Anthropic API tool that lets Claude see a desktop through screenshots and operate it with mouse and keyboard. Use when automating GUI workflows, browser automation without CSS selectors, desktop app testing, or any task that requires seeing and interacting with a graphical interface.

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Blender's compositor post-processes renders with a node graph, and this skill scripts it from Python (bpy) in Blender 5.x. Use when the user wants to set up compositor nodes, add post-processing effects, color correct renders, combine render passes, apply blur or glare, key green screens, write passes to multilayer EXR, or port a compositing script that broke after Blender 5.0 (scene.node_tree, CompositorNodeComposite, glare_type and file_slots are gone).

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Babylon.js is an open-source 3D engine for the browser that renders with WebGL or WebGPU and includes a scene graph, PBR materials, glTF loading, Havok physics, a GUI layer and WebXR. Use when a user asks to build a 3D scene, game, product configurator or VR/AR experience with Babylon.js, load a glTF/GLB model, add physics or in-scene UI, switch to WebGPU, or shrink a Babylon.js bundle.

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